Cytogenetics meets phylogenetics: A review of karyotype evolution in diprotodontian marsupials

Journal of Heredity

Volumn 101, Issue 6, 2010, Pages 690-702

  Westerman, Michael ^a   Meredith, Robert W ^b   Springer, Mark S ^b  

^a LA TROBE UNIVERSITY   (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

diprotodontia; marsupial evolution; marsupial karyotypes; molecular phylogeny

Indexed keywords

ARTICLE; CENTROMERE; CHROMOSOME 1; CHROMOSOME 2; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 6; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CYTOGENETICS; GENE SEQUENCE; HERBIVORE; KARYOTYPE EVOLUTION; MARSUPIAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PERICENTRIC CHROMOSOME INVERSION; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; BIOLOGICAL EVOLUTION; CENTROMERE; CHROMOSOME ABERRATIONS; CHROMOSOME FRAGILE SITES; CHROMOSOMES, MAMMALIAN; CYTOGENETIC ANALYSIS; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC DRIFT; GENETIC MARKERS; GENETIC VARIATION; INCISOR; INTERSPERSED REPETITIVE SEQUENCES; KARYOTYPING; MARSUPIALIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

BURRAMYIDAE; CAENOLESTIDAE; DASYUROMORPHIA; DIDELPHIMORPHIA; DIPROTODONTIA; METATHERIA; MICROBIOTHERIA; PERAMELEMORPHIA; VOMBATIDAE;

EID: 77958523684     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esq076     Document Type: Article

References (69)

1. Allshire RC, Karpen GH. 2008. Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet. 9:923-937.
2. Archer M. 1982. Genesis: and in the beginning there was an incredible carnivorous mother. In: Archer M, editor. Carnivorous marsupials. Vol. 1. Chipping Norton NSW (Australia): Royal Zoological Society of NSW, Surrey Beatty and Sons. p. vii-x.
3. Baird AB, Hillis DM, Patton JC, Bickham JW. 2009. Speciation by monobrachial centric fusions: a test of the model using nuclear DNA sequences from the bat genus Rhogeessa. Mol Phylogenet Evol. 50:256-267.
4. Baverstock PR, Adams M, Archer M, Mc Kenzie NL, How R 1983. An electrophoretic and chromosomal study of the dasyurid marsupial genus Ningaui Archer. Aust J Zool. 31:381-392.
5. Boyle S, Gilchrist S, Bridger J M, Mahy NL, Ellis JA, Bickmore WA. 2001. The spatial organisation of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet. 10:211-219.
6. Bridger JM, Boyle S, Kill IR, Bickmore WA. 2000. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol. 10:149-152.
7. Bulazel K, Ferreri GC, Eldridge MDB, O'Neill RJ. 2007. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol. 8:R170.
8. Bulazel K, Metcalfe C, Ferreri GC, Yu J, Eldridge MDB, O'Neill RJ. 2006. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics. 172:1129-1137.
9. Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, et al. 2009. A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma. 118:113-125.
10. Cremer M, Von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T. 2001. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 9:541-567.
11. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. 1999. Differences in the localisation and morphology of chromosomes in the human nucleus. J Cell Biol. 145:1119-1131.
12. Deakin JE, Graves JAM. 2010. Mapping genes on tammar wallaby target chromosomes. In: Coulson G, Eldridge M, editors. Macropods: the biology of kangaroos, wallabies and rat-kangaroos. Melbourne (Australia): CSIRO Publishing. p. 3-12.
13. Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, van den Hurk C, Pask AJ, et al. 2008. Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosomes Res. 16:1159-1175.
14. Donnellan SC. 1989. The chromosomes of five species of Phalanger (Marsupialia: Phalangeridae). Aust Mammal. 12:69-72.
15. Eichler EE, Sankoff D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science. 301:793-797.
16. Eldridge MDB, Close RL. 1993. Radiation of chromosome shuffles. Curr Opin Genet Dev. 3:915-922.
17. Eldridge MDB, Johnston PG. 1993. Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae), VIII. An investiga-tion of the non-random nature of karyotypic change. Genome. 36: 524-534.
18. Ferguson-Smith MA. 1997. Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications. Eur J Hum Genet. 5:253-265.
19. Ferreri GC. 2008. An ultra-conserved retrovirus and its impact on vertebrate genome evolution [dissertation]. [Storrs (CT)]: University of Connecticut.
20. Ferreri GC, Liscinsky DM, Mack JA, Eldridge MDB, O'Neill RJ. 2005. Retention of latent centromeres in the mammalian genome. J Hered. 96:217-224.
21. Ferreri GC, Marzelli M, Rens W, O'Neill RJ. 2004. A centromere specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenet Genet Res. 107:115-118.
22. Glas R, deLeo AA, Delbridge M, Reid K, Ferguson-Smith MA, O'Brien PCM, Westerman M, Graves JAM. 1999. Chromosome painting in marsupials: genomic conservation in the kangaroo family. Chromosome Res. 7:167-176.
23. Graves JAM, Westerman M. 2002. Marsupial genetics and genomics. Trends Genet. 18:517-521.
24. Greaves IK, Rens W, Ferguson-Smith MA, Griffin D, Graves JAM. 2003. Conservation of chromosome arrangement and position of the X in mammalian sperm suggests functional significance. Chromosome Res. 11:503-513.
25. Greaves IK, Svartman M, Wakefield M, Taggart D, De Leo A, Ferguson-Smith MA, Rens W, O'Brien PC, Voullaire L, Westerman M, et al. 2001. Chromosomal painting detects non-random chromosome arrangement in dasyurid marsupial sperm. Chromosome Res. 9:251-259.
26. Hayman DL. 1990. Marsupial cytogenetics. Aust J Zool. 37:331-339.
27. Hayman DL, Martin P. 1974. Mammalia 1: Monotremata and Marsupialia. In: John B, editor. Animal cytogenetics. Volume 4. Chordata 4'. Berlin (Germany): Gebruder Borntraege.
28. Hayman DL, Rofe RH, Sharp PJ. 1987. Chromosome evolution in marsupials. Chromosomes Today. 9:91-102.
29. Jansa SA, Forsman J F, Voss RS. 2006. Different patterns of selection on the nuclear genes IRBP and DMP-1 affect the efficiency but not the outcome of phylogeny estimation for didelphid marsupials. Mol Phylogenet Evol. 33:368-380.
30. Jansa SA, Voss RS. 2000. Phylogenetic studies on didelphid marsupials I. Introduction and preliminary results from nuclear IRBP gene sequences. J Mammal Evol. 7:43-77.
31. Kipling D, Warburton PE. 1997. Centromeres, CENP-B and Tigger too. Trends Genet. 13:141-145.
32. Le Beau MM, Rowley JD. 1984. Heritable fragile sites in cancer. Nature. 308:607-608.
33. Manuelidis L, Borden J. 1988. Reproducible compartmentalisation ofindividual chromosome domains in human CNS cells revealed by in situ hybridization and three dimensional reconstruction. Chromosoma. 96:397-410.
34. Meaburn KJ, Misteli T. 2007. Chromosome territories. Nature. 445:379-381.
35. Meredith RW, Mendoza M, Roberts KK, Westerman M, Springer MS. 2010. A phylogeny and timescale for Pseudocheirid (Marsupialia: Diprotodontia) evolution in Australia and New Guinea. J Mammal Evol. 17:75-99.
36. Meredith RW, Westerman M, Case J A, Springer MS. 2008. A phylogeny and timescale for marsupial evolution based on sequences for five nuclear genes. J Mamm Evol. 15:1-26.
37. Meredith RW, Westerman M, Springer M. 2008. Phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes: Marsupialia) based on nuclear sequences. Aust J Zool. 56:1-16.
38. Meredith RW, Westerman M, Springer M. 2009. A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes. Mol Phylogenet Evol. 59:554-571.
39. Metcalfe CJ, Bulazel K, Ferreri GC, Schroeder-Reiter E, Warner G, Rens W, Obergfell C, Eldridge MDB, O'Neill RJ. 2007. Genomic instability within centromeres ofinterspecific marsupial hybrids. Genetics. 177:2507-2517.
40. Nagele RG, Freeman T, Mc Morrow L, Thomson Z, Kitson-Wind K, Lee H. 1999. Chromosomes exhibit preferential positioning in nuclei of quiescent human cells. J Cell Sci. 112:525-535.
41. Okada T, Ohzeki J, Nakano M, Yoda K, Brinkley WR, Larionov V, Masumoto H. 2007. CENP-B controls centromere function depending of chromatin context. Cell. 131:1287-1300.
42. O'Neill RJ, Eldridge MDB, Metcalfe CJ. 2004. Centromere dynamics and chromosome evolution in marsupials. J Hered. 95:375-381.
43. O'Neill RJW, Eldridge MDB, Toder R, Ferguson-Smith MA, Graves JAM. 1999. Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the Tammar wallaby and rock wallaby spp with the 2n\22 ancestral macropodid karyotype. Genome. 42:525-530.
44. O'Neill RJ, O'Neill MJ, Graves JAM. 1998. Undermethylation associated with retroelement activation and chromosome remodelling in an in-terspecific mammalian hybrid. Nature. 393:68-72.
45. Rens W, O'Brien PCM, Fairclough H, Harman L, Graves JAM, Ferguson-Smith MA. 2003. Reversal and convergence in marsupial chromosome evolution. Cytogenet Genome Res. 102:282-290.
46. Rens W, O'Brien PCM, Graves JAM, Fergusson-Smith MA. 2003. Localization of chromosome regions in potoroo nuclei (Potorous tridactylus, Marsupialia: Potoroinae). Chromosoma. 112:66-76.
47. Rens W, O'Brien PCM, Yang F, Graves JAM, Ferguson-Smith MA. 1999. Karyotype relationships between four distantly related marsupials revealed by reciprocal chromosome painting. Chromosome Res. 7:461-474.
48. Rens W, O'Brien PCM, Yang F, Solansky N, Perelman P, Graphodatsky AS, Ferguson-Smith MWJ, Svartman M, De Leo AA, Graves JAM, et al. 2001. Karyotypic relationships between distantly related marsupials from South America and Australia. Chromosome Res. 9:301-308.
49. Rofe RH. 1978. G-banded chromosomes and the evolution of Macro-podidae. Aust Mammal. 2:53-63.
50. Rofe RH. 1979. G-banding and chromosome evolutionin marsupials. [Ph D thesis]. South Australia: University of Adelaide.
51. Rofe RH, Hayman D. 1985. G-banding evidence for a conserved complement in the Marsupialia. Cytogenet Cell Genet. 39:40-50.
52. Sharman GB. 1961. The mitotic chromosomes of marsupials and their bearing on taxonomy and phylogeny. Aust J Zool. 9:38-60.
53. Sharman GB. 1982. Karyotypic similarities between Dromiciops australis (Microbiotheriidae, Marsupialia) and some Australian marsupials. In: Archer M, editor. Carnivorous marsupials. Vol. 1. Chipping Norton NSW (Australia): Royal Zoological Society of NSW, Surrey Beatty and Sons. p. 711-714.
54. Sharman GB, Close RL, Maynes GM. 1990. Chromosome evolution, phylogeny and speciation of rock wallabies (Petrogale: Macropodidae). Aust J Zool. 37:351-363.
55. Sherwin W, Graves JAM. 2006. What marsupials can do for genetics and what genetics can do for marsupials. In: Armati PJ, Dickman CR, Hume ID, editors. Marsupials. Cambridge: Cambridge University Press. p. 22-82.
56. Specchia V, Piacentini L, Tritto P, Fanti L, D'Alessandro R, Palumbo G, Pimpinelli S, Bozzetti MP. 2010. Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons. Nature. 463:662-665.
57. Spotorno AE, Marin J-C, Yevenes M, Walker LI, Fernandez-Donoso R, Pincheira R, Soledad Berrios M, Palma AE. 1997. Chromosome Divergences among American marsupials and the Australian affinities of the American Dromiciops. J Mammal Evol. 4:259-269.
58. Springer MS, Krajewski CW, Meredith RW. 2009. Marsupials. (Metatheria). In: Hedges SB, Kumar S, editors. The Timetree of life. Oxford, UK: Oxford University Press. p. 466-470.
59. Stamatakis A. 2006. RAx M L-VI-HPC: maximum likelihood-based phylo-genetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688-2690.
60. Svartman M. 2009. American marsupials chromosomes: why study them. Genomics Mol Biol. 32:675-687.
61. Svartman M, Vianna-Morgante AM. 1998. Karyotype evolution of marsupials: from higher to lower diploid numbers. Cytogenet Cell Genet. 82:263-266.
62. Tanabe H, Muller S, Neusser M, von Hase J, Calgano E, Cremer M, Solovei I, Cremer C, Cremer T. 2002. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Nat Acad Sci USA. 93:10200-10205.
63. Toder R, O'Neill RJW, O'Brien PCM, Voullaire L, Graves JAM. 1997. Comparative chromosome painting between two marsupials: origins of an XX/XY1Y2 sex chromosome system. Mamm Genome. 8:418-422.
64. Voss RS, Jansa SA. 2009. Phylogenetic relationships and classification of didelphid marsupials, an extant radiation of New World mammals. Bull Am Mus Nat Hist. 322:1-177.
65. Waters PD, Dobigny G, Wadell PJ, Robinson TJ. 2007. Evolutionary history of LINE-1 in the major clades ofplacental mammals. PLo S ONE. 2:e158.
66. Westerman M, Woolley PA. 1990. Cytogenetics of some New Guinean dasyurids and genome evolution in the Dasyuridae (Marsupialia). Aust J Zool. 37:521-531.
67. White ME. 1994. After the greening: the browning of Australia. New South Wales (Australia): Kangaroo Press.
68. Yunis JJ. 1986. The chromosomal basis of human neoplasia. Science. 223:227-235.
69. Zalenskaya IA, Zalenskaya AO. 2004. Non-random positioning of chromosomes in human sperm nuclei. Chrom Res. 12:163-173.